EBI_TCoffee

Created: 2008-06-03 06:31:37 Last updated: 2010-12-06 11:02:53

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Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSTCoffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) is used.

Note: the WSTCoffee service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement T-COFFEE services (REST or SOAP) should be used instead.

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Workflow Components

Inputs (2)

Name	Description
Email_address	User e-mail address.
Sequences	Sequences to align, fasta format recommended.

Processors (7)

Name	Type	Description
runTCoffee	arbitrarywsdl	Submit a T-Coffee analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee#runtcoffee_params_content)
Job_params	local	T-Coffee parameters
Contents_list	local	Wrap input data in list.
Input_data	local	Add type information to input.
EBI_TCoffee_poll_job	workflow	Check job status
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee#poll_jobid_type)
Unpack_alignment	local	Convert byte[] from service into string.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done	Map job status to true/false	job_status	is_done

Outputs (2)

Name	Description
TCoffee_job_ID	EBI job identifer.
TCoffee_alignment	T-Coffee alignment in a ClustalW style format.

Links (10)

Source	Sink
Email_address	Job_params:email
Contents_list:output	runTCoffee:content
Input_data:output	Contents_list:WSArrayofData
Job_params:output	runTCoffee:params
Sequences	Input_data:content
Get_alignment:output	Unpack_alignment:bytes
Unpack_alignment:string	TCoffee_alignment
runTCoffee:jobid	EBI_TCoffee_poll_job:Job_ID
runTCoffee:jobid	Get_alignment:jobid
runTCoffee:jobid	TCoffee_job_ID

Coordinations (1)

Controller	Target
EBI_TCoffee_poll_job	Get_alignment

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

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Hamish McWilliam

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Information Featured In Packs (2)

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EMBL-EBI Web Services (retired)

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Information Statistics

2413 viewings

2488 downloads

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Version History

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EBI_TCoffee

Created by Hamish McWilliam on Tuesday 03 June 2008 06:31:37 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 11:02:53 (UTC)

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